Links
ELK Stack - An excellent Guide for Ubuntu 14.04 is at https://www.digitalocean.com/community/tutorials/how-to-install-elasticsearch-logstash-and-kibana-elk-stack-on-ubuntu-14-04 TESTET
TopBeat - https://www.digitalocean.com/community/tutorials/how-to-gather-infrastructure-metrics-with-topbeat-and-elk-on-ubuntu-14-04 TESTET
PacketBeat - https://z0z0.me/monitor-your-servers-with-elasticsearch-2-x-and-beats-and-display-it-in-kibana/ TESTET
GeoIP Support - https://www.digitalocean.com/community/tutorials/how-to-map-user-location-with-geoip-and-elk-elasticsearch-logstash-and-kibana NOT TESTET
Tomcat Log Parsing - https://blog.lanyonm.org/articles/2014/01/12/logstash-multiline-tomcat-log-parsing.html NOT TESTET
Tips
Make sure the server time is correct for all servers 
as in use NTP.
This actually gave me a problem where logstash => ElasticSearch did not work
Sample filebeat config for my Confluence Server
Sample filebeat config for my Alfresco Server
Other Stuff:
http://www.slideshare.net/aca_it/monitor-your-atlassian-stack-like-the-nsa